IonCram is the first compression tool that efficiently compresses the Ion Torrent BAM files. IonCram extends the popular CRAM program by improving the compression of the flow signals. IonCram could improve the compression of CRAM by 13% achieving an overall space saving of about 45%.

IonCram uses different compression techniques for compressing the flow signal(gzip, bzip2, xz, and zstd ). To use zstd, Please install it(https://github.com/facebook/zstd) and make it system available.

apt-get install g++ libncurses5-dev  parallel python3 make libbz2-dev zstd zlib1g-dev liblzma-dev automake libtool samtools time
./configure --binDir <install directory>
make
make install

If install directory is not supplied "ioncram/build/" will be used

yum -y install https://centos7.iuscommunity.org/ius-release.rpm
yum  -y install  gcc-c++ compat-gcc-32 compat-gcc-32-c++ ncurses-devel parallel xz-devel bzip2-devel make zlib-devel automake zstd file libtool samtools time python34u

./configure --binDir <install directory>
make
make install

If install directory is not supplied "ioncram/build/" will be used

gzip -d test_data/chrY.fa.gz
./ioncram compress -i test_data/test1.bam -r test_data/chrY.fa -c -o test1.ioncram

./ioncram compress -i input.bam -o compressed.IonCram -r hg19.fa

./ioncram decompress -i compressed.IonCram -o original.bam -r hg19.fa

Scripts to calculate statisitics about the flowsignal and compression ratio of CRAM and ioncram can be found under scripts/ folder.

Scripts take the folder as argument where the ioncram binaries are installed.

scripts/flowSignalInBam.sh <binaries folder> <bam file>

scripts/scrambleStatistics.sh <binaries folder> <bam file> <reference file>

scripts/ionStatistics.sh <binaries folder> <bam file> <reference file> <compression tool>

Compression tools supported are : gzip, xz, and zstd.

ioncram has five commands compress, decompress, compare, version, and cite, You can list the available commands by "./ioncram --help". Every command has its own help page.

Tool for compressing SAM/BAM into IonCram format.

./ioncram compress [options] -i <input SAM/BAM> -r <input reference FASTA> -o <outputfile>

• -i , --input-file : * File name of the input file can be SAM/BAM
• -o , --output-file: * File name of the output IonCram file
• -r , --reference: * Reference fasta file used by CRAM compression. Should be the same reference used in the mapping phase

• -b , --bed-file: * reads overlapping this BED FILE
• -c , --check: * Check the compressed file and compare it with the original
• -z , --compression: * Compression technique used to compress Flow signal. Options are xz, gzip, bzip2, and zstd. xz is the default technique
• -v , --verbose: * Verbose mode prints the size used by every field in the l_data
• -l , --lossy: * Lossy mode discard the highly repeated reads and uses only one read to represent.
• -d , --deez: * Use deez tool instead of samtools and CRAM

Tool for decompressing IonCram into BAM format

./ioncram decompress -i <input IonCram> -r <input reference FASTA> -o <outputfile bam>

• -i , --input-file : * File name of the input file can be SAM/BAM
• -o , --output-file: * File name of the output IonCram file
• -r , --reference: * Reference fasta file used by CRAM compression. Should be the same reference used in the mapping phase

Tool for comparing SAM/BAM/IonCram files

./ioncram compare -i1 <input file1> -i2 <input file1> -r <input reference FASTA>

• -i1 , --input-file1 : * File name of the input file can be SAM/BAM/CRAM/IonCram
• -i2 , --input-file2 : * File name of the input file can be SAM/BAM/CRAM/IonCram
• -r , --reference: * Reference fasta file used by CRAM compression. Should be the same reference used in the mapping phase

Shokrof, M., Abouelhoda, M. IonCRAM: a reference-based compression tool for ion torrent sequence files. BMC Bioinformatics 21, 397 (2020). https://doi.org/10.1186/s12859-020-03726-9

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